[maker-devel] Fewer genes in MAKER 2.31.3

[Shaun Jackman]

Hi, Carson. I’m annotating a 6 Mbp plant mitochondrial genome using GenBank
coding nucleotide and protein sequences from related species. I’m seeing 50
genes annotated using MAKER 2.31, and 37 genes annotated using MAKER
2.31.3. The missing genes look good based on the evidence. I see
protein_match evidence in the 2.31.3 GFF file, but no resulting gene and
mRNA.

Is there a ChangeLog indicating the changes from 2.31 to 2.31.3? Do you
know of a change that might cause this? What information can I give you
that would help debug this? My maker_opts.ctl file follows.

Cheers,
Shaun

#-----Genome (these are always required)
genome=pg29mt-concat.fa #genome sequence (fasta file or fasta embeded
in GFF3 file)
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----EST Evidence (for best results provide a file for at least one)
est=cds_na.fa #set of ESTs or assembled mRNA-seq in fasta format

#-----Protein Homology Evidence (for best results provide a file for
at least one)
protein=cds_aa.fa #protein sequence file in fasta format (i.e. from
mutiple oransisms)

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=picea #select a model organism for RepBase masking in RepeatMasker
rmlib=rmlib.fa #provide an organism specific repeat library in fasta
format for RepeatMasker
repeat_protein=/usr/local/opt/maker/libexec/data/te_proteins.fasta
#provide a fasta file of transposable element proteins for
RepeatRunner

#-----Gene Prediction
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no

protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no

#-----External Application Behavior Options
cpus=4 #max number of cpus to use in BLAST and RepeatMasker (not for
MPI, leave 1 when using MPI)

#-----MAKER Behavior Options
est_forward=1 #map names and attributes forward from EST evidence, 1 =
yes, 0 = no
single_exon=1 #consider single exon EST evidence when generating
annotations, 1 = yes, 0 = no
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140505/e138d53a/attachment-0002.html>